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root/OpenMD/branches/development/src/integrators/VelocityVerletIntegrator.cpp

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.cpp (file contents), Revision 1126 by gezelter, Fri Apr 6 21:53:43 2007 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 50 | Line 51
51		#include "integrators/VelocityVerletIntegrator.hpp"
52		#include "integrators/DLM.hpp"
53		#include "utils/StringUtils.hpp"
54	+	#include "utils/ProgressBar.hpp"
55
56	<	namespace oopse {
56	>	namespace OpenMD {
57		VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
58		dt2 = 0.5 * dt;
59		rotAlgo = new DLM();
#	Line 65 | Line 67 | namespace oopse {
67
68		void VelocityVerletIntegrator::initialize(){
69
70	<	forceMan_->init();
70	>	forceMan_->initialize();
71
72		// remove center of mass drift velocity (in case we passed in a
73		// configuration that was drifting)
74		velocitizer_->removeComDrift();
75
76		// initialize the forces before the first step
77	<	calcForce(true, true);
77	>	calcForce();
78
79		// execute the constraint algorithm to make sure that the system is
80		// constrained at the very beginning
81		if (info_->getNGlobalConstraints() > 0) {
82		rattle->constraintA();
83	<	calcForce(true, true);
83	>	calcForce();
84		rattle->constraintB();
85		//copy the current snapshot to previous snapshot
86		info_->getSnapshotManager()->advance();
#	Line 94 | Line 96 | namespace oopse {
96
97		dumpWriter->writeDumpAndEor();
98
99	<	if (simParams->getUseSolidThermInt()) {
100	<	restWriter = createRestWriter();
99	<	restWriter->writeZAngFile();
100	<	}
101	<
99	>	progressBar = new ProgressBar();
100	>
101		//save statistics, before writeStat,  we must save statistics
102		thermo.saveStat();
103		saveConservedQuantity();
104	+	if (simParams->getUseRNEMD())
105	+	rnemd_->getStarted();
106	+
107		statWriter->writeStat(currentSnapshot_->statData);
108
109		currSample = sampleTime + currentSnapshot_->getTime();
110	<	currStatus =  statusTime + currentSnapshot_->getTime();;
110	>	currStatus =  statusTime + currentSnapshot_->getTime();
111		currThermal = thermalTime + currentSnapshot_->getTime();
112		if (needReset) {
113		currReset = resetTime + currentSnapshot_->getTime();
114		}
115	+	if (simParams->getUseRNEMD()){
116	+	currRNEMD = RNEMD_exchangeTime + currentSnapshot_->getTime();
117	+	}
118		needPotential = false;
119		needStress = false;
120
121		}
122	<
122	>
123		void VelocityVerletIntegrator::doIntegrate() {
124
125
#	Line 127 | Line 132 | namespace oopse {
132		integrateStep();
133
134		postStep();
135	<
135	>
136		}
137
138		finalize();
#	Line 138 | Line 143 | namespace oopse {
143		void VelocityVerletIntegrator::preStep() {
144		RealType difference = currentSnapshot_->getTime() + dt - currStatus;
145
146	<	if (difference > 0 || fabs(difference) < oopse::epsilon) {
146	>	if (difference > 0 || fabs(difference) < OpenMD::epsilon) {
147		needPotential = true;
148		needStress = true;
149		}
#	Line 158 | Line 163 | namespace oopse {
163		currThermal += thermalTime;
164		}
165		}
166	<
166	>	if (useRNEMD) {
167	>	if (currentSnapshot_->getTime() >= currRNEMD) {
168	>	rnemd_->doRNEMD();
169	>	currRNEMD += RNEMD_exchangeTime;
170	>	}
171	>	rnemd_->collectData();
172	>	}
173	>
174		if (currentSnapshot_->getTime() >= currSample) {
175		dumpWriter->writeDumpAndEor();
176	<
165	<	if (simParams->getUseSolidThermInt())
166	<	restWriter->writeZAngFile();
167	<
176	>
177		currSample += sampleTime;
178		}
179	<
179	>
180		if (currentSnapshot_->getTime() >= currStatus) {
181		//save statistics, before writeStat,  we must save statistics
182		thermo.saveStat();
183		saveConservedQuantity();
184	+
185	+	if (simParams->getUseRNEMD()) {
186	+	rnemd_->getStatus();
187	+	}
188	+
189		statWriter->writeStat(currentSnapshot_->statData);
190	<
190	>
191	>	progressBar->setStatus(currentSnapshot_->getTime(), runTime);
192	>	progressBar->update();
193	>
194		needPotential = false;
195		needStress = false;
196		currStatus += statusTime;
197		}
198	<
199	<	if (needReset && currentSnapshot_->getTime() >= currReset) {
200	<	resetIntegrator();
201	<	currReset += resetTime;
202	<	}
186	<
198	>
199	>	if (needReset && currentSnapshot_->getTime() >= currReset) {
200	>	resetIntegrator();
201	>	currReset += resetTime;
202	>	}
203		}
204
205
206		void VelocityVerletIntegrator::finalize() {
207		dumpWriter->writeEor();
208
193	–	if (simParams->getUseSolidThermInt()) {
194	–	restWriter->writeZAngFile();
195	–	delete restWriter;
196	–	restWriter = NULL;
197	–	}
198	–
209		delete dumpWriter;
210		delete statWriter;
211
#	Line 207 | Line 217 | namespace oopse {
217		void VelocityVerletIntegrator::integrateStep() {
218
219		moveA();
220	<	calcForce(needPotential, needStress);
220	>	calcForce();
221		moveB();
222		}
223
224
225	<	void VelocityVerletIntegrator::calcForce(bool needPotential,
226	<	bool needStress) {
217	<	forceMan_->calcForces(needPotential, needStress);
225	>	void VelocityVerletIntegrator::calcForce() {
226	>	forceMan_->calcForces();
227		}
228
229		DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
#	Line 225 | Line 234 | namespace oopse {
234
235		std::string statFileFormatString = simParams->getStatFileFormat();
236		StatsBitSet mask = parseStatFileFormat(statFileFormatString);
237	<
238	<	// if solidThermInt is true, add extra information to the statfile
239	<	if (simParams->getUseSolidThermInt()){
237	>
238	>	// if we're doing a thermodynamic integration, we'll want the raw
239	>	// potential as well as the full potential:
240	>
241	>
242	>	if (simParams->getUseThermodynamicIntegration())
243		mask.set(Stats::VRAW);
244	+
245	+	// if we've got restraints turned on, we'll also want a report of the
246	+	// total harmonic restraints
247	+	if (simParams->getUseRestraints()){
248		mask.set(Stats::VHARM);
249		}
250
251		if (simParams->havePrintPressureTensor() &&
252		simParams->getPrintPressureTensor()){
253	<	mask.set(Stats::PRESSURE_TENSOR_XX);
254	<	mask.set(Stats::PRESSURE_TENSOR_XY);
255	<	mask.set(Stats::PRESSURE_TENSOR_XZ);
256	<	mask.set(Stats::PRESSURE_TENSOR_YX);
257	<	mask.set(Stats::PRESSURE_TENSOR_YY);
258	<	mask.set(Stats::PRESSURE_TENSOR_YZ);
259	<	mask.set(Stats::PRESSURE_TENSOR_ZX);
260	<	mask.set(Stats::PRESSURE_TENSOR_ZY);
261	<	mask.set(Stats::PRESSURE_TENSOR_ZZ);
253	>	mask.set(Stats::PRESSURE_TENSOR_XX);
254	>	mask.set(Stats::PRESSURE_TENSOR_XY);
255	>	mask.set(Stats::PRESSURE_TENSOR_XZ);
256	>	mask.set(Stats::PRESSURE_TENSOR_YX);
257	>	mask.set(Stats::PRESSURE_TENSOR_YY);
258	>	mask.set(Stats::PRESSURE_TENSOR_YZ);
259	>	mask.set(Stats::PRESSURE_TENSOR_ZX);
260	>	mask.set(Stats::PRESSURE_TENSOR_ZY);
261	>	mask.set(Stats::PRESSURE_TENSOR_ZZ);
262		}
263
264		if (simParams->getAccumulateBoxDipole()) {
#	Line 250 | Line 266 | namespace oopse {
266		mask.set(Stats::BOX_DIPOLE_Y);
267		mask.set(Stats::BOX_DIPOLE_Z);
268		}
269	+
270	+	if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
271	+	if (simParams->getPrintTaggedPairDistance()) {
272	+	mask.set(Stats::TAGGED_PAIR_DISTANCE);
273	+	}
274	+	}
275
276	<	return new StatWriter(info_->getStatFileName(), mask);
277	<	}
276	>	if (simParams->getUseRNEMD()) {
277	>	mask.set(Stats::RNEMD_EXCHANGE_TOTAL);
278	>	}
279	>
280
281	<	RestWriter* VelocityVerletIntegrator::createRestWriter(){
258	<	return new RestWriter(info_);
281	>	return new StatWriter(info_->getStatFileName(), mask);
282		}
283
284
285	<	} //end namespace oopse
285	>	} //end namespace OpenMD

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.cpp (property svn:keywords), Revision 1126 by gezelter, Fri Apr 6 21:53:43 2007 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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